Intelligent Design

Is Photosynthesis Irreducibly Complex?

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From Nature this week. “Knowing how plants and bacteria harvest light for photosynthesis so efficiently could provide a clean solution to mankind’s energy requirements. The secret, it seems, may be the coherent application of quantum principles. Roseanne J. Sension doi:10.1038/446740a Full Text 

Photosynthesis provides the primary energy source for almost all life on Earth. One of its remarkable features is the efficiency with which energy is transferred within the light harvesting complexes comprising the photosynthetic apparatus. Suspicions that quantum trickery might be involved in the energy transfer processes at the core of photosynthesis are now confirmed by a new spectroscopic study. The study reveals electronic quantum beats characteristic of wavelike energy motion within the bacteriochlorophyll complex from the green sulphur bacterium Chlorobium tepidum. This wavelike characteristic of the energy transfer process can explain the extreme efficiency of photosynthesis, in that vast areas of phase space can be sampled effectively to find the most efficient path for energy transfer.
 
Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated. The energy transfer mechanism is often described by semiclassical models that invoke ‘hopping’ of excited-state populations along discrete energy levels 1, 2. Spectroscopic data clearly document the dependence of the dominant energy transport pathways on the spatial properties of the excited-state wavefunctions of the whole bacteriochlorophyll complex 6, 10. Here we obtain direct evidence for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system. The quantum coherence manifests itself in characteristic, directly observable quantum beating signals among the excitons within the Chlorobium tepidum FMO complex at 77 K. This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path. Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems Gregory S. Engel et al Nature 446, 782-786 (12 April 2007) | doi:10.1038/nature05678″

Conclusion? Obviously this is a brilliant piece of design by someone who even knows how quantum mechanics works. Well not exactly …
Photosynthesis Analysis Shows Work Of Ancient Genetic Engineering 

Science Daily 2002 — The development of the biochemical process of photosynthesis is one of nature’s most important events, but how did it actually happen? This is a question that molecular biology has first posed, and now perhaps answered.
“The process of photosynthesis is a very complex set of interdependent metabolic pathways,” said Robert Blankenship, professor of biochemistry at Arizona State University. “How it could have evolved is a bit mysterious.

Photosynthesis is one of the most important chemical processes ever developed by life — a chemical process that transforms sunlight into chemical energy, ultimately powering virtually all the living things and allowing them to dominate the earth. The evolution of aerobic photosynthesis in bacteria is also the most likely reason for the development of an oxygen-rich atmosphere that transformed the chemistry of the Earth billions of years ago, further triggering the evolution of complex life. After decades of research, biochemists now understand that this critical biological process depends on some very elaborate and rapid chemistry involving a series of enormously large and complex molecules a set of complex molecular systems all working together.
We know that the process evolved in bacteria, probably before 2.5 billion years ago, but the history of photosynthesis’s development is very hard to trace,” said Blankenship.

In a paper in the November 22 2002 issue of Science, Blankenship and colleagues partially unravel this mystery through an analysis of the genomes of five bacteria representing the basic groups of photosynthetic bacteria and the complete range of known photosynthetic processes.

The analysis revealed clear evidence that photosynthesis did not evolve through a linear path of steady change and growing complexity but through a merging of evolutionary lines that brought together independently evolving chemical systems — the swapping of blocks of genetic material among bacterial species known as horizontal gene transfer.

“We found that the photosynthesis-related genes in these organisms have not had all the same pathway of evolution. It’s clear evidence for horizontal gene transfer,” said Blankenship.

Blankenship performed a mathematical analysis of the set of shared genes to determine possible evolutionary relationships between them, but they arrived at different results depending on which genes were tested
“We did a kind of tree analysis of all 188 genes to determine what the best evolutionary tree was. We found that a fraction of the genes supported each of the different possible arrangements of the tree. It’s clear that the genes themselves have different evolutionary histories,” Blankenship said.

Blankenship argues that different pieces of the system evolved separately in different organisms, perhaps to serve purposes different from their current function in the photosynthesis. Brought together either by fusion of two different bacteria or by the “recruitment” of blocks of genes, the new combination of genes resulted in a new combined system.

“This kind of evolution in bacteria is kind of like what happens at a junk dealer,” said Blankenship.

“Bits and pieces of whatever there is out in the yard get hauled back and welded together and made into this new thing. All these metabolic pathways get borrowed and bent a bit and changed.”

Blankenship points out that nature’s way of creating useful and complicated chemical systems through horizontal gene transfer also points to how human-directed biodesign might co-opt the process.

“This work gives us some insights into how complex metabolic pathways originated and evolved, so this might give some ideas about how to engineer new pathways into microorganisms,” he said. “These organisms could be designed to carry out new types of chemistry that may benefit mankind, such as multi-step synthesis of drugs.”

How exactly did all those different organisms, who donated parts of the photosynthesetic process, get their energy while they were doing all that evolving of the components of the Irreducibly Complex looking system ready to be put together by the Blind Watchmaker?

25 Replies to “Is Photosynthesis Irreducibly Complex?

  1. 1
    Jehu says:

    How exactly did all those different organisms, who donated parts of the photosynthesetic process, get their energy while they were doing all that evolving of the components of the Irreducibly Complex looking system ready to be put together by the Blind Watchmaker?

    They didn’t. I am sorry but I don’t buy the horizontal gene transfer story. What is clear in the article that you post is that there is no evidence of evolution of photosynthasis other than that it exists. The rest of the article strikes me as “just so” story telling.

  2. 2
    gpuccio says:

    “This kind of evolution in bacteria is kind of like what happens at a junk dealer,” said Blankenship.

    “Bits and pieces of whatever there is out in the yard get hauled back and welded together and made into this new thing. All these metabolic pathways get borrowed and bent a bit and changed.”

    Very funny example, for a random process of cooption!

    Personally, I have never been able to buy anything useful at a junk dealer, least of all put them together for some new purpose. But you know, I am not a good buyer, nor a good coopter. I definitely lack the talent.

    But, certainly, I do know people who are able to buy stuff at the junk dealer, or just find it anywhere, and build up what nobody would expect. I really admire that kind of people. They have a precious talent. They are creative, manipulative, artistic, original. They produce utility and beauty where nothing could be anticipated. Obviously, they have to really manipulate the things they buy, so that they can be put together and work in a new, unprecedented pattern. Obviously, they must choose among lots of junk at the junk dealer, but you know, they have that “magic” eye which allows them to see what nobody sees, and sometimes just adding some small piece of junk they have at home, to be just the right “pivot” for the new creation, will do the trick.

    May be you can detect some envy in my words, and you are not wrong. Those guys are truly wonderful people. Everybody loves them, hoping maybe that they will some time receive from them some self-made, artistic, unexpect gift for their sitting room. Hey, these people just go around, creatively spreading design everywhere…

    Oh, I know… I should not have used that word… I always say embarassing things!

    So, to apologize, I have just made up a new motto: “cooption happens!”. May if I repeat it frequently enough, I could even believe it.

  3. 3
    Latemarch says:

    I’m beginning to think that co-option and lateral transfer should be thought of as the cutting up and recombining of parts (typically at the paragraph level, where a single coherent idea represents a single functional protein.) of the “D”and”E” volumes of the encyclopedia to get the “F” volume…….uh, yeah, that’ll work.

  4. 4
    pk4_paul says:

    There is no question about photosynthesis being IC. But it’s worse than that from an evolutionary perspective. There are 17 enzymes alone involved in the synthesis of chlorophyll. Are we to believe that all intermediates had selective value? Not when some of them form triplet states that have the same effect as free radicals like O2. In addition if chlorophyll evolved before antenna proteins, whose function is to bind chlorophyll, then chlorophyll would be toxic to cells. Yet the binding function explains the selective value of antenana proteins. Why would such proteins evolve prior to chlorophyll and if they did not how would cells survive chlorophyll until they did?

  5. 5
    rrf says:

    Did the authors calculate CSI? If not that would be a great project for some of the scientists here.

  6. 6
    shaner74 says:

    “This kind of evolution in bacteria is kind of like what happens at a junk dealer”

    LOL! Really? It is? So, a “jumk dealer” is capable of taking parts and combining them together using principles of quantum mechanics to efficiently acquire energy from the sun? In all seriousness, I’m beginning to think that Walter Remine might be on to something with his “Biotic Message” idea. What a sad state it is when we’re the only ones that can see design when it’s so blatantly obvious. If our “scientific community” had any b*lls, they would throw darwin in the garbage and get on with science.

  7. 7
    Jon Jackson says:

    “We found that the photosynthesis-related genes in these organisms have not had all the same pathway of evolution. It’s clear evidence for horizontal gene transfer,” said Blankenship.

    Aren’t they assuming the very thing they’re trying to prove? Oh, wait, the proof of evolution is already a done deal. My bad.

  8. 8
    mentok says:

    We see very clearly a case where “evolution” is being used as a substitute for “magic”. Just like with magic there is nothing that evolution cannot do if you are willing to give evolution powers that a supposedly undirected “nature” shouldn’t have i.e. creating fantastic things out of pretty much thin air.

  9. 9
    Jehu says:

    In sum, photosynthesis is a process that converts sunlight into energy used by the cell with nearly 100% efficiency. The complex that accomplishes this feat requires 188 genes to construct. Molecular phylogenetics has produced no evidence of evolution, as you can produce 188 different trees of how it was produced. This leaves horizontal gene transfer as the only possilbe explanation besides design. The problem with HGT is that it can never be demonstrated. It is just this magical event that happened in the past where 188 genes came together, with slight modifications, to create an energy gathering mechanism of an astonishing 100% efficiency.

  10. 10
    phonon says:

    Jehu, depending on how the calculation is done, the light conditions, and the species of plant, the efficiency of photosynthesis is usually found to be 6-30%.

  11. 11
    Jehu says:

    phonon,

    Not according to this article.

    Through photosynthesis, green plants and cyanobacteria are able to transfer sunlight energy to molecular reaction centers for conversion into chemical energy with nearly 100-percent efficiency . Speed is the key – the transfer of the solar energy takes place almost instantaneously so little energy is wasted as heat. How photosynthesis achieves this near instantaneous energy transfer is a long-standing mystery that may have finally been solved.

    http://physorg.com/news95605211.htm

  12. 12
    Jehu says:

    Okay, it looks like I misread the article. Here is the answer from a different article.,

    Photosynthesis is the most important biological process on Earth. It serves as the World’s largest solar battery. The primary reactions have close to 100% quantum efficiency (i.e., one quantum of light leads toone electron transfer); and under most ideal conditions, the overall energy efficiency can reach 35%

    http://www.life.uiuc.edu/govindjee/whatisit.htm

  13. 13
    idnet.com.au says:

    35% efficiency is much higher than the best intelligently designed solar cells. Perhaps we need to go down to the junk yard and find out how to improve solar cells.

  14. 14
    idnet.com.au says:

    As I see it, photosynthesis involves a specially designed complex which initially captures light to energise a chemical “battery”. The captured energy can then be used by specific molecular machine complexes, to split apart and reconfigure molecules (CO2 and H2O). In life, the process is coupled to the production of carbohydrates and oxygen for metabolism.

    The build up of O2 in the earth’s early atmosphere shows that there is way more energy available from the sun than is needed for reproduction and food.

    O2 in the atmosphere represents accumulation of a waste product from a process that is very efficient. All the carbon stores in the biosphere are another waste product. Burning fuel is eliminating waste from photosynthesis and returning to the original H2O and CO2.

    The energy crisis could be solved if we were able to use a modified photosynthesis complex to either just form H2 and O2, or store charge separation (a battery), or to form CH4 or C2H6 and O2. No more green house gases, no more globaal warming crisis.

    We need Intelligent Designers modifying the Intelligent Designer’s designs.

  15. 15
    Designed Jacob says:

    “How exactly did all those different organisms, who donated parts of the photosynthetic process, get their energy while they were doing all that evolving of the components of the Irreducibly Complex looking system ready to be put together by the Blind Watchmaker?”

    Even a created bacterium would need food starting out. You know their answer will be “the primordial soup”, which will inevitably have all the essential contents and structure of an egg, which structure of course had not evolved yet.

  16. 16
    Designed Jacob says:

    “The energy crisis could be solved if we were able to use a modified photosynthesis complex to either just form H2 and O2, or store charge separation (a battery), or to form CH4 or C2H6 and O2. No more green house gases, no more global warming crisis.”

    What’s gonna be emitted when you burn the methane and ethane?

  17. 17
    mike1962 says:

    idnet.com.au, “no more global warming crisis.”

    How so, given that global warming has nothing to do with human activity?

  18. 18
    Bob O'H says:

    idnet.com.au – Methane is a greenhouse gas as well, and one that has a worse effect than C02.

    Bob

  19. 19
    idnet.com.au says:

    The point I was making is that if you make H2 and O2 there is no greenhouse effect. If you mahe methane to burn you have no net greenhouse gas effect either as you take a carbou out for each carbon you put in a methane molecule.

    The problem with greenhouse gasses, if there is a problem, is that we are getting sequested carbon from under the ground and putting it into the atmosphere as CO2.

    The processes I describe would be the ultimate clean technology. Sun in and energy out with a neutral effect on CO2.

  20. 20
    phonon says:

    Jehu,

    I see now that there is a great deal of variation in the way efficiency is calculated. Depending on where you draw the lines. Once the photon reaches the chlorophyll the quantum efficiency is near 100%. I think the low efficiency values are for total energy from total light. Not all photons reach the chlorophyll and the chemical reactions are not very efficient. So, the photosystem protein complexes are near 100% at converting photon energy to electron transfer energy. That’s probably what you meant in the first place.

    idnet.com.au,

    There are people working on solar cells that use photosystem I and II as light harvesters. It’s still in its infancy.

    http://www.pnas.org/cgi/content/full/103/14/5251

  21. 21
    idnet.com.au says:

    Thanks phonon, I liked the statement in the pnas paper “Whether devices are completely synthetic and mimic biological processes or devices use natural biomolecules, much of the research for future power systems will happen at the intersection of disciplines.”

  22. 22
    Falco says:

    I have a question about irreducible complexity that I can’t get out of my head with regards to the IC of the bacterial flagellum.

    I recently learned that horizontal gene transfer and not darwinian evolution is respobsible for bacteria developing immunities. How does this apply to the evolution of the flagellum itself? Would horizontal gene transfer speed the process of spreading mutations through the population (and at least theoretically speed up evolution).

  23. 23
    idnet.com.au says:

    Horizontal gene transfer is a way of explaining why evolutionary trees fail to obey standard evolutionary theory.

    HGT is a process where by organisms cooperate in the process of filling environments.

    The ultimate materialistic explanation for “useful”genes that are worth swapping remains mutation and natural selection.

    The problem of IC and the flagellum is that parts of a whole need to be fitted together. They must all have a useful, selectable function in their donor organism.

    It might be argued that if three societies independantly developed technologies (or spelling/language for that matter) and then combined their resources, it would be very unlikely that there would be much compatibility between the groups.

    The linear measures would be different. The nuts and bolts would have different threads and different diameters. The electrical equipment would have different voltages and if AC would work at different frequencies, to name but a few problems.

    If HGT plays a role in biology, and it seems it does, at least with plasmids in bacteria, it infers that there are rules set for biological systems, specifications if you like, which as far as we can tell, are not intrinsic/essential to matter. These standards are yet another mark of Intelligently Designed systems.

  24. 24
    314 says:

    You are confusing some issues, Dave.

    For example, biology has many interoperable parts despite significant divergence.

    Further, while biology may create the metaphorical “metric and english” measurement” divide, it is certainly possible for me to make use of metric screws despite by predilection for enlish measurement.

    Sufficient application of hammers and english screwdrivers get a metric screw in place.

    Partial utiliity, even with poorly adapted tools, can still create an evolutionary benefit.

  25. 25
    gpuccio says:

    314:

    The point is that HGT has no role in creating information. It is only a tool, however important, of information redistribution in a bacterial population. But that information must be already there.

    The idea of cooption, either through traditional evolution or through HGT, is logically undefendable, as we have discussed many times on this blog. The whole idea that single “parts” of an IC system, each one already extremely complex and unlikely of itself, can arise for different and separate reasons, in the same organism or in different organisms, and the, all at once, be “remixed” so that a new function, IC in principle, can arise, either as a result of pure RM + NS, or with the “help(??)” of HGT, is totally unbelievable: it is only a stupid way to fool stupid readers so that they can be convinced that Behe’s idea of IC has been in some way answered.
    That’s a lie, and only a lie. Behe’s idea of IC has not been answered, in any way. The idea of cooption is so ridiculous that only desperation can have convinced darwinists to this last resource to defend their castle of improbabilities and impossibilities from the devastating effects of the sound arguments of IC.
    The fact is, if a system is so complex and IC that tehre is no way to build it reasonably through RM and NS directly, buiding it in separate parts and for different functions is much more unlikely and impossible. Darwinists seem to constantly forget that functions do not grow everywhere like mushrooms. You don’t just take a piece of one function, a little bit of another, a slice of a third, mix them up and here is a new, complex, IC system ready for use. And at that point, please, ask nature to select it!
    Darwinists dream of functions arising at their request wherever they need them, but that’s not what happens in real life. In real life, function, complex function, is a rare treasure in a desert, and it requires a reasonable explanation.
    Regarding the concept of “interoperable parts despite significant divergence”, it is obvious that you make a lot of free assumptions about that. I will only say that interoperable parts are a very recurrent trait of design, and not of randomness. Every good designer uses interoperable parts, where it is appropriate, and modifies them when appropriate. And no good designer operates through rough application of hammers and scewdrivers to get a screw in place where it does not fit. That’s only an example of bad design (I would call it stupid obstinacy) apllied by an intelligent (more or less) agent to accomplish a non productive task, where any good designer would have used the appropriate tools, just as it happens in nature.

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